R/str_chunk_reorder.R

In MiguelRodo/VaccCompData: Data package for novel TBV vaccine comparison paper

#' Locate all occurrences of all strings in a character vector.
#'
#' \code{str_locate_multi} provides the a sorted vector
#' of the locations of character elements (or strings) in a character
#' string.
#'
#' @param string character. String to search through.
#' @param pattern character vector. Vector of strings to search for in \code{string}.
#' @return Numeric vector of found positions for any character in \code{pattern},
#' sorted in ascending order.
#' @examples
#' str_locate_multi( "abcdeabcdexyza", c( "ab", "x" ) )

str_locate_multi = function( string, pattern ){
  lapply( as.list( pattern ), function(x) str_locate_all( string, x ) ) %>%
    unlist() %>%
    unique() %>%
    sort()
}

#' Find the border positions of the characters to split for.
#'
#' \code{str_split_chunk_pos} provides a list, where
#' each element is a length-two integer vector of the
#' locations at which \code{string} must be split at
#' to create sub-strings (or chunks), where the right-hand
#' endpoints of thhe chunks are at an element of
#' \code{pattern}.
#'
#' @inheritParams str_locate_multi
#' @return A list with each element an ordered integer
#' vector containing the start and end position of each
#' chunk.
#' @examples
#' str_split_chunk_pos( "abcdeabcdexyza", c( "a", "x" ) )

str_split_chunk_pos = function( string, pattern ){
  posVec = str_locate_multi( string, pattern )
  if( length( posVec ) == 0 ) return( list( c( 1, str_length( string ) ) ) )
  chunkBorderPosList = list( c( 1, posVec[1] ) )
  lapply( 1:( length(posVec)-1 ), function( i ){
    chunkBorderPosList[[ i + 1 ]] <<- c( posVec[ i ] + 1, posVec[ i + 1] )
  })
  chunkBorderPosList
}

#' Split a string into chunks.
#'
#' \code{str_split_chunk} works like str_split, except that it:
#' \itemize{
#'   \item allows detection of multiple characters, and
#'   \item includes the characters from \code{pattern} in the
#'   chunks.
#' }
#' @return A list of strings.
#' @examples
#' str_split_chunk( "GpTpIL2nIL17p", c( "p", "n" ) )

str_split_chunk = function( string, pattern ){
  chunkBorderPosList = str_split_chunk_pos( string, pattern )
  lapply( 1:length( chunkBorderPosList ), function(i) str_sub( string,
    chunkBorderPosList[[i]][1],  chunkBorderPosList[[i]][2] ) )
}


#' Re-order chunks in a string.
#'
#' \code{str_chunk_reorder_string} re-orders the chunks of a
#' string.
#'
#' @inheritParams str_locate_multi
#' @param order integer vector. The chunk originally in the i-th position
#' in \code{string} is placed in the \code{order[i]}-th position.
#' @return A string.
#' @examples
#' str_chunk_reorder_string( "GpTpIL2nIL17p", c( "p", "n" ), c( 1, 3, 2, 4 ) )

str_chunk_reorder_string = function( string, pattern, order ){
  chunkList = str_split_chunk( string, pattern )
  if( length( order ) != length( chunkList ) ) stop( "Number of chunks implied by order not equal to number of chunks defined by pattern.")
  outString = chunkList[[ which( order == 1 ) ]]
  if( length( order ) > 1 ){
    plyr::l_ply( 2:length( order ), function( i ){
      outString <<- str_c( outString, chunkList[[ which( order == i ) ]] )
    } )
  }
  outString
}

#' Re-order chunks in a string.
#'
#' \code{str_chunk_reorder} re-orders the chunks of a string, and is vectorised.
#'
#' @inheritParams str_locate_multi
#' @inheritParams str_chunk_reorder_string
#'
#' @return A string, or a character vector.
#' @examples
#' str_chunk_reorder( "GpTpIL2nIL17p", c( "p", "n" ), c( 1, 3, 2, 4 ) )
#' str_chunk_reorder ( c( "GpTpIL2nIL17p", "GpTpIL2nIL17n" ),  c( "p", "n" ), c( 1, 3, 2, 4 ) )
#' @export

str_chunk_reorder = function( string, pattern, order ){
  plyr::laply( string, function(x){
    str_chunk_reorder_string( x, pattern, order )
  }  )
}